Every website has an information architecture. This involves the information flow of your website and how navigation will be laid. This is a preliminary step and while the final design may stray, this is a basic starting point. Sometimes this information takes the form of an outline rather than a chart.
Once you decide what pages you wish to include on your website it is just a matter of putting them in a logical order. Basic user interface design uses proven ways of how people expect a website to work. As far as your web layout, a good rule of thumb is not making them think. Usually simple is better.